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Identification of main and epistatic QTLs and QTL through environment interactions for eating and cooking quality in Iranian rice

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Abstract

Breeding new rice varieties with high Eating and Cooking Quality (ECQ) characteristics is an important goal in rice breeding programs. To this end, 242 Recombinant Inbred Lines (RILs) of two populations derived from Alikazemi/IR67017-180-2-1-2 and Alikazemi/Saleh crosses were evaluated in two environments. The main and epistatic QTLs and QTL × Environment (Q × E) interactions were analyzed using the Mixed-Model-based Composite Interval Mapping method. A total of 17 main QTLs with additive effects were mapped on 6 rice chromosomes, including 6 QTLs for Amylose Content, 5 QTLs for Gelatinization Temperature and 6 QTLs for Gel Consistency. Seven QTLs were found on chromosome 6 associated with a common RM4128 marker (close to the Alk locus) influencing the ECQ characteristics with favorable alleles from the common female parent. Five QTL clusters were identified on chromosome 6, 7, 8, and 9, suggesting that the co-located QTLs with pleiotropic effects may control ECQ traits. A major QTL cluster was found for AC and GC between RM4128 and RM549 markers close to the Alk locus on chromosome 6, which is in the vicinity of another QTL located in RM587-RM4128 interval. 13 QTL pairs were identified to have a significant epistatic, Additive × Additive effects involved in controlling ECQ traits. A small phenotypic variation was found for the epistatic QTLs and Q × E interactions, suggesting the complexity of ECQ inheritance traits in rice. Further comprehensive studies and validation of the detected QTLs could be useful for marker-assisted selection to improve grain quality in rice.

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References

  • Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard J (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa× O. glaberrima. Theor Appl Genet 109:630–639

    Article  CAS  PubMed  Google Scholar 

  • Arif M (2002) Molecular mapping of genes/QTLs affecting resistance to Xanthomonas oryzae pv. oryzae (Ex. Ishiyama) Swings et al and grain quality traits in rice (Oryza sativa L.). Ph.D thesis, University of Philippines in Los Banos. Philippines

  • Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality of rice. J Sci Food Agric 24:1589–1594

    Article  CAS  PubMed  Google Scholar 

  • Cao G, Zhu J, He C, Gao Y, Yan J, Wu P (2001) Impact of epistasis and QTL× environment interaction on the developmental behavior of plant height in rice (Oryza sativa L.). Theor Appl Genet 103:153–160

    Article  CAS  Google Scholar 

  • Cheng A, Ismail I, Osman M, Hashim H (2014) Mapping of quantitative trait loci for aroma, amylose content and cooked grain elongation traits in rice. Plant Omics 7:152

    CAS  Google Scholar 

  • DelaCruz N, Khush GS (2000) Rice grain quality evaluation procedures. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. New Delhi, India: Oxford and IBH Publishing Co. Pvt. Ltd, pp 15–29

  • DelaCruz N, Kumar I, Kaushik R, Khush G (1993) Effect of temperature during grain development on stability of cooking quality components in rice [Oryza sativa]. Jap J Breed 39(3):299–306

    Google Scholar 

  • Ebadi A-A, Farshadfar E, Rabiei B (2013) Mapping QTLs controlling cooking and eating quality indicators of Iranian rice using RILs across three years. Aust J Crop Sci 7:1494

    Google Scholar 

  • Fan C, Yu X, Xing Y, Xu C, Luo L, Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110:1445–1452

    Article  CAS  PubMed  Google Scholar 

  • Gao Z, Zeng D, Cui X, Zhou Y, Yan M, Huang D, Li J, Qian Q (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China Ser C Life Sci 46:661–668

    Article  CAS  Google Scholar 

  • Gao Z, Zeng D, Cheng F, Tian Z, Guo L, Su Y, Yan M, Jiang H, Dong G, Huang Y (2011) ALK, the Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice F. J Integr Plant Biol 53:756–765

    CAS  PubMed  Google Scholar 

  • Gao FY, Zeng LH, Qiu L, Lu XJ, Ren JS, Wu XT, Su XW, Gao YM, Ren GJ (2015) QTL mapping of grain appearance quality traits and grain weight using recombinant inbred populations in rice (Oryza sativa L.). J Integr Agr 4:1961–1968

    Google Scholar 

  • Hao W, Zhu MZ, Gao JP, Sun SY, Lin HX (2009) Identification of quantitative trait loci for rice quality in a population of chromosome segment substitution lines. J Integr Plant Biol 51:500–512

    Article  CAS  PubMed  Google Scholar 

  • Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He P, Li S, Qian Q, Ma Y, Li J, Wang W, Chen Y, Zhu L (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502–508

    Article  CAS  Google Scholar 

  • Hosseini M, Houshmand S, Mohamadi S, Tarang A, Khodambashi M, Rahimsoroush H (2012) Detection of QTLs with main, epistatic and QTL× environment interaction effects for rice grain appearance quality traits using two populations of backcross inbred lines (BILs). Field Crops Res 135:97–106

    Article  Google Scholar 

  • ISIRI (2005) Rice-specifications and test methods. Iranian National Standard (2nd revision), Institute of Standards and Industrial Research of Iran, Karaj, Iran

  • Juliano B (1971) A simplified assay for milled rice amylose. Cereal Sci Today 16:334–360

    Google Scholar 

  • Kosambi DD (2016) The estimation of map distances from recombination values. DD Kosambi. Springer, pp 125–130

  • Kumar I, Khush G (1988) Inheritance of amylose content in rice (Oryza sativa L.). Euphytica 38:261–269

    Article  CAS  Google Scholar 

  • Kumar K, Kumar M, Kim S-R, Ryu H, Cho Y-G (2013) Insights into genomics of salt stress response in rice. Rice 6:27

    Article  PubMed  PubMed Central  Google Scholar 

  • Lanceras JC, Huang ZL, Naivikul O, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105). DNA Res 7:93–101

    Article  CAS  PubMed  Google Scholar 

  • Liang Z, Bin L, Zhang KP, Tian JC, Deng ZY (2009) Detection of QTLs with additive effects, epistatic effects, and QTL× environment interactions for zeleny sedimentation value using a doubled haploid population in cultivated wheat. Agr Sci China 8:1039–1045

    Article  Google Scholar 

  • Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35:111–126

    CAS  Google Scholar 

  • Liu BH (2017) Statistical genomics: linkage, mapping, and QTL analysis. CRC Press, Boca Raton

    Book  Google Scholar 

  • Liu L, Yan X, Jiang L, Zhang W, Wang M, Zhou S, Shen Y, Shen Y, Liu S, Chen L (2008) Identification of stably expressed quantitative trait loci for cooked rice elongation in non-Basmati varieties. Genome/National Research Council Canada = Genome/Conseil national de recherches Canada 51:104–112

  • Lou J, Chen L, Yue G, Lou Q, Mei H, Xiong L, Luo L (2009) QTL mapping of grain quality traits in rice. J Cereal Sci 50:145–151

    Article  CAS  Google Scholar 

  • Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932

    Article  CAS  PubMed  Google Scholar 

  • McCouch S, Cho Y, Yang M, Paul E, Blinstrub M, Morishima H, Kinoshita T (1997) Suggestion for QTL nomenclature. Rice Genet Newsl 14:11–13

    Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  CAS  PubMed  Google Scholar 

  • Murray M, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qiu X, Du B, Hu H, Ou X, Lv W, Yang L, Xing D, Xu J, Zheng T, Xu J (2017) Scanning QTLs for Grain Shape using Two Sets of Introgression Lines in Rice. Int J Agric Biol 19:509–516

    Article  Google Scholar 

  • Sabouri H (2009) QTL detection of rice grain quality traits by microsatellite markers using an indica rice (Oryza sativa L.) combination. J Genet 88:81–85

    Article  PubMed  Google Scholar 

  • Sabouri A, Rabiei B, Toorchi M, Aharizad S, Moumeni A (2012) Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Aust J Crop Sci 6(5):808–814

    Google Scholar 

  • Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467–473

    Article  CAS  PubMed  Google Scholar 

  • SAS (2003) SAS Procedures Guide: Version 9. Sas Inst

  • Soroush HR, Eshraghi A, Salehi MM, Ali AJ, Nahvi M, Allahgholipour M, Erfani A, Tarang A, Eghlidi A, Padasht F (2005) Kadous: an aromatic, high-yielding variety with good cooking quality. Int Rice Res Notes 30:16–17

    Google Scholar 

  • Su Y, Rao Y, Hu S, Yang Y, Gao Z, Zhang G, Liu J, Hu J, Yan M, Dong G (2011) Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.). Theor Appl Genet 123:859

    Article  PubMed  Google Scholar 

  • Sun SY, Hao W, Lin HX (2006) Identification of QTLs for cooking and eating quality of rice grain. Rice Sci 13:161–169

    Google Scholar 

  • Tang S, Khush G, Juliano B (1991) Genetics of gel consistency in rice (Oryza sativa L.). J Genet 70:69–78

    Article  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCOUCH SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Tian R, Jiang GH, Shen LH, Wang LQ, He Y-Q (2005) Mapping quantitative trait loci underlying the cooking and eating quality of rice using a DH population. Mol Breed 15:117–124

    Article  CAS  Google Scholar 

  • Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Umemoto T, Aoki N (2005) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme. Funct Plant Biol 32:763–768

    Article  CAS  PubMed  Google Scholar 

  • Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y (2002) Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theor Appl Genet 104:1–8

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Liu W, Xu Y, He Y, Luo L, Xing Y, Xu C, Zhang Q (2007) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 115:463–476

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Pang Y, Zhang J, Zhang Q, Tao Y, Feng B, Zheng T, Xu J, Li Z (2014) Genetic background effects on QTL and QTL× environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice. Crop J 2:345–357

    Article  Google Scholar 

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch S (1997) Chromosomal regions associated with segregation distortion of molecular markers in F 2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545

    Article  CAS  PubMed  Google Scholar 

  • Yacouba NT, Yu B, Gao G, Zhang Q, Xu C, Xiao J, He Y (2013) QTL analysis of eating quality and cooking process of rice using a new RIL population derived from a cross between Minghui 63 and Khao Dawk Mali105. Aust J Crop Sci 7:2036–2047

    Google Scholar 

  • Yan B, Yacouba NT, Chen J, Wang Y, Gao G, Zhang Q, Liu X, He Y (2014) Analysis of minor quantitative trait loci for eating and cooking quality traits in rice using a recombinant inbred line population derived from two indica cultivars with similar amylose content. Mol Breed 34:2151–2163

    Article  CAS  Google Scholar 

  • Yang J, Zhu J (2005) Methods for predicting superior genotypes under multiple environments based on QTL effects. Theor Appl Genet 110:1268–1274

    Article  PubMed  Google Scholar 

  • Yu Y, Wing RA, Li J (2013) Grain quality. Genetics and genomics of rice. pp 237–254. Springer, Berlin

  • Yun BW, Kim MG, Handoyo T, Kim KM (2014) Analysis of rice grain quality-associated quantitative trait loci by using genetic mapping. Am J Plant Sci 5:1125–1132

    Article  Google Scholar 

  • Yun YT, Chung CT, Lee YJ, Na HJ, Lee JC, Lee SG, Lee KW, Yoon YH, Kang J-W, Lee HS (2016) QTL mapping of grain quality traits using introgression lines carrying Oryza rufipogon chromosome segments in japonica rice. Rice 9:62

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Luo L, Xu C, Zhang Q, Xing Y (2006) Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor Appl Genet 113:361–368

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Ou X, Hu H, Du B, Lv W, Yang L, Xing D, Xu J, Qiu X, Zheng T (2018) Identification of QTLs for yield-related traits using two sets of introgression lines with a common donor parent in rice. Int J Agri Biol 20:15–24

    Google Scholar 

  • Zhao X, Zhou L, Ponce K, Ye G (2015) The usefulness of known genes/Qtls for grain quality traits in an indica population of diverse breeding lines tested using association analysis. Rice 8:29

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Authors sincerely appreciate the Rice Research Institute staff for their excellent help in conducting this study.

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Authors and Affiliations

  1. Agronomy and Plant Breeding Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran

    Hossein Rahimsoroush, Farhad Nazarian-Firouzabadi & Ahmad Ismaili

  2. Rice Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran

    Maryam Hosseini Chaloshtari & Ali Akbar Ebadi

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  1. Hossein Rahimsoroush
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  2. Farhad Nazarian-Firouzabadi
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  3. Maryam Hosseini Chaloshtari
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  4. Ahmad Ismaili
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  5. Ali Akbar Ebadi
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Contributions

HRS carried out the QTL analysis. FNF, MHC, AI and AAE designed and wrote the manuscript.

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Correspondence to Farhad Nazarian-Firouzabadi.

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Rahimsoroush, H., Nazarian-Firouzabadi, F., Chaloshtari, M.H. et al. Identification of main and epistatic QTLs and QTL through environment interactions for eating and cooking quality in Iranian rice. Euphytica 217, 25 (2021). https://doi.org/10.1007/s10681-020-02759-8

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  • DOI: https://doi.org/10.1007/s10681-020-02759-8

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